What I understand is that Windows 7 will not install on GPT (GUID Partition Table) drives. Of course, all new Macs have their drives partitioned that way, and when you run the boot camp assistant, it is taking advantage of the GPT to resize your main partition on the fly and free up some space for the Windows installer to create an NTFS (or whatever) partition.
Of course, it doesn't wipe out your disk and repartition with MBR (Master Boot Record) since all of your data is intact at the end. So, I think the assistant is adding an MBR alongside the GPT, or creating some kind of hybrid partition table?
Second: It's easy enough to use Disk Utility to resize your main partition and leave free space. Is it possible to "manually" do whatever else Boot Camp Assistant is doing to prep the drive for Windows?
Context: Mid-2010 iMac Core i5, Mac OS X 10.7.4, Boot Camp 4.0.3, Windows 7.